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genescf / GeneSCF

Gene Set Clustering based on Functional annotation
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using "-m=update" yields empty database files? #19

Closed joe-marturano closed 8 months ago

joe-marturano commented 1 year ago

Hi, thank you for this excellent library, I've used it successfully for several years. Today I tried the "-m=update" command with GO_BP and goa_human, e.g.,:

./GeneSCF-1.1-p3.beta/geneSCF -m=update -i="./GeneSCF-1.1-p3.beta/io/xxxxx.csv" -o="./GeneSCF-1.1-p3.beta/io/" -t=gid -db=GO_BP -bg=20000 --plot=no, -org=goa_human

But this seemingly failed to unpack the files correctly. It produced a gzip error:

/GeneSCF-1.1-p3.beta/class/lib/db/goa_human/gene_association.goa_human.gz: unexpected end of file

and yielded empty files (ls -l):

image

.

I tried using /prepare_database but received the same result. My workaround was a fresh install with the -m=normal parameter, which returned successfully. Could you please investigate and advise? Thank you.

decodebiology commented 8 months ago

Hi,

The Gene Ontology database was revised with some changes in the database structure. A recent version of GeneSCF will resolve this issue. I assume your fresh installation worked out. If not let me know. Otherwise, I will close this issue in the next 10 days.

joe-marturano commented 8 months ago

Great thanks for the explanation. And yes a fresh installation worked great. Feel free to close.